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Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB

Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB

  1. G. L. Andersen1,*
  1. 1Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A-3317, Berkeley, California 94720
  2. 2Microbial Ecology Program, DOE Joint Genome Institute, 2800 Mitchell Drive, Bldg. 400-404, Walnut Creek, California 94598
  3. 3Danish Genome Institute, Gustav Wieds vej 10 C, DK-8000 Aarhus C, Denmark
  4. 4Department of Bioinformatics, Baylor University, P.O. Box 97356, 1311 S. 5th St., Waco, Texas 76798-7356
  5. 5Department of Bioengineering, University of California, Berkeley, California 94720
  6. 6Departments of Biochemistry and Mathematics, The University of Queensland, Brisbane, Queensland 4072, Australia
  7. 7Department of Computer Science, Chalmers University of Technology, SE-412 96 Göteborg, Sweden

ABSTRACT

A 16S rRNA gene database (http://greengenes.lbl.gov) addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. It was found that there is incongruent taxonomic nomenclature among curators even at the phylum level. Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria.

FOOTNOTES

    • Received 20 December 2005.
    • Accepted 15 April 2006.
  • *Corresponding author. Mailing address: Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A-3317, Berkeley, CA 94720. Phone: (510) 495-2795. Fax: (510) 486-7152. E-mail: GLAndersen{at}lbl.gov.